During President Obama's recent participation in the Southeast Asian Nations' Summit in Bali, he emphasized Indonesia's strategic importance as one of Asia's fastest-growing economies and a valuable U.S. ally in trade. This recognition may strike indigenous communities in the Papuan provinces of Indonesia as a cruel irony. Their own security and advancement has been crippled by a steady onslaught of human rights abuses at the hands of the Indonesian government, most in the name of economic development.

As Indonesia's value to the U.S. economy increases -- particularly with the new multibillion-dollar Boeing deal President Obama celebrated during the Summit -- will the United States turn a blind eye to the harm Indonesia's development strategy will do to Papuans and the environment?

Indonesia's exploitation of rich Papuan lands and their impoverished indigenous owners reveals the dark but little-known underbelly of the country's development ambitions. This exploitation stretches back half a century.

Since Indonesia took control of Papua from the Dutch in 1969, the state has committed widespread human rights violations against indigenous Papuans, including extrajudicial killings, torture, and sexual violence. By encouraging non-Papuan Indonesians to migrate to the territory, the government is quickly rendering Papuans a minority in their own land. Unsustainable development policies and unfettered natural resource extraction have devastated Papua's ecosystems.

These abuses continue despite legislation in 2001 granting Papua "Special Autonomy." The government justifies violence against civilians by invoking a threat to security from Papuan separatist movements. Last month, the Indonesian military opened fire on an unarmed crowd gathered for the Papuan People's Congress, a council of customary Papuan leaders. The military arrested hundreds of Congress participants; the bodies of three participants with bullet wounds were later found near the meeting's location. Media censorship and a virtual ban on foreign visitors have not prevented reports of this and other attacks on civilians by the police and military.

Last Tuesday, Secretary of State Clinton voiced U.S. concern for the "violence and abuse of human rights" in Papua, calling for "continuing dialogue and political reforms in order to meet the legitimate needs of the Papua people." As violence escalates, world leaders should press the Indonesian government on the long-term, less conspicuous abuses of Papuan rights: government-sanctioned mass seizure of indigenous land for the purpose of natural resource extraction and large-scale agriculture for export.

Plans for Indonesia's latest "mega-project" in Papua-the Merauke Integrated Food and Energy Estate, or MIFEE-call for converting up to 2 million hectares of largely primary forest and protected wetlands to agricultural use. The government has already invited more than 30 multinational companies to invest a projected US $8.6 billion in developing agricultural plantations for producing rice and biofuel. In place of forests rich with the animal and plant life necessary for their subsistence, Papua's tribal groups will soon find a desert of industrial agricultural and a pollution-filled landscape no longer fit for their survival.

Last May, Yale Law School's Lowenstein International Human Rights Clinic conducted an investigatory trip to Papua to document these abuses. Interviews with indigenous Papuan communities, NGOs, and government leaders foreshadowed the devastating effects that MIFEE will wreak on Papuans and their environment.

Indigenous Papuans are the lawful owners of the lands designated for the MIFEE mega-project. Their cultural identity and livelihood are intimately bound to lands they have stewarded for generations. MIFEE will rupture this heritage and jeopardize the health and cultural survival of Papuan communities. As one leader of the local Malind tribe told us, "The land and people are inseparable, but the MIFEE project tries to sever them. If you take the land, it means that the clan too is destroyed."

MIFEE targets an area of land ecologically unsuited for large-scale agriculture. It will destroy much of Papua's unique biodiversity and cause substantial soil erosion. Already, Papua-based NGOs have reported flooding, contamination of drinking waters, and food shortages.

These problems are not just matters of local concern. Deforestation in the tropics is the second leading contributor to human-induced carbon dioxide emissions. Indonesia -- the world's third largest carbon-dioxide emitter -- has promised the international community to cut its greenhouse gas pollutants. Fulfilling these promises is essential to the success of anti-deforestation programs in developing countries. MIFEE will directly contravene Indonesia's environmental commitments, turning Papua's ancient forests from a vital store of carbon dioxide into a massive contributor to global climate change.

In June 2010, President Obama and President Yudhoyono entered into a Comprehensive Partnership to fortify U.S.-Indonesian relations. The Partnership includes joint efforts to mitigate climate change and a significant US-sponsored aid package to bolster Indonesian development. The United States must accompany such investments in Indonesia's future with an expectation of responsible development and respect for the basic rights of indigenous Papuans.

The ASEAN summit highlighted the importance of the U.S. relationship with Indonesia. As the first U.S. President to attend the ASEAN Summit, President Obama signaled a new era of economic and political ties with the world's most populous Muslim country. These advances must not come at the expense of Indonesia's democratic and human rights obligations. As U.S. relations with Indonesia deepen, the Papuan people will be relying on us -- and President Obama -- to speak out against Indonesian development practices that come with an unacceptably heavy price tag.

Jim Silk is a clinical professor of law at Yale Law School, where he teaches the Allard K. Lowenstein International Human Rights Clinic. Last May, Professor Silk led a team of three Lowenstein Clinic students on an investigatory field mission to Papua, Indonesia. The team examined the impacts of Papuan development on the region's indigenous communities, and the Clinic's research will be published in a forthcoming human rights report.

Professor Silk is also executive director of the Law School's Orville H. Schell, Jr. Center for International Human Rights. He was formerly the director of the Robert F. Kennedy Memorial Center for Human Rights, where, in addition to guiding the organization's advocacy, his work focused on human rights in China, child labor, and corporate responsibility. Following law school, Jim practiced at a firm in Washington, D.C. His pro bono work included representing a Virginia death row inmate in his appeals.